Upstream TigerVNC uses ~/.vnc to store its configuration (among other things). We've patched ours to not use that configuration as we have our own. Unfortunately our viewer still tries to create the directory each start, which isn't really correct. Seen with 4.13.0, but has probably been around since at least 2011.
TigerVNC has now started respecting XDG directories, so we should be seeing ~/.config/tigervnc and similar instead.